Medicine, agriculture, and other biology-related industries increasingly depend on the information contained in genomic DNA. Advancing our understanding of how genes are structured and regulated will eventually lead to novel therapeutics for combating cancer and other diseases, to cheaper and more nutritious food, and to less wasteful materials and energy sources. Sequencing genomes is now a relatively straightforward task. Annotating them, however, is proving to be a much more difficult one, especially for eukaryotic genomes. The gene catalogs of all but the simplest eukaryotic genomes are still incomplete, even for well-known organisms with a long history of genetics and molecular biology. Because annotations are the focal point for many kinds of research and technological applications, it is essential that they be correct. Incomplete and incorrect annotations poison every experiment that employs them. We believe the key to improving genome annotation lies in better software for the creation and quality control of genome annotations. This proposal describes our design for a system we call GenomeInvestigator. GenomeInvestigator consists of three components: MAKER, EVALUATOR and VERIFIER. MAKER creates genome annotations, EVALUATOR performs quality control analyses on extant annotations, and VERIFIER automatically designs experiments to problematic portions of annotations. By analogy to genome sequencing, MAKER and EVALUATOR produce draft annotation with quality values, and VERIFIER directs annotation finishing efforts. GenomeInvestigator is designed to be easily portable and will be freely available. Its outputs will be Sequence Ontology compliant and GMOD compatible. Medicine, agriculture, and other biology-related industries increasingly depend on the information contained in genomic DNA. Advancing our understanding of how genes are structured and regulated will eventually lead to novel therapeutics for combating cancer and other diseases, to cheaper and more nutritious food, and to less wasteful materials and energy sources.